Ten months before the main events of the story, the movie opens up to the devastated City Of Townsville before cutting to the Central City police station, where dozens of officers are reacting in a combination of stunned shock and panic, with a news feed revealing over eleven million people hace died due to a nuclear bome detonating in the heat of the city. The crmera slowly closes up on a heavily guarded interrogation room, where maniacal laughter can be heard from inside revealing the culprit behind this genocide: Dr. Eggman.

Dr.Eggman is being interrogated by Sonic, who demands to know why would he build a weapon like that, but Eggman refuses to give a straight answer. As Sonic lunges over the table to grab Eggman, a well behind the two explodes violently...revealing a teenage Blossom, her eyes burning red with restrained heat vision. She orders Sonic away from Eggman, dispite Sonic assuring her that he is handling the situation. The leader of the Powerpuff Girls stalks towards the madman before violently tossing the table between herself and Eggman aside, grabbing him, and shoving him against the two way mirror of the room. Blossom rants about being drugged before despondently moaning a little boy she once rescued. Eggman mockingly points out both Bunny's death and Townsville's destruction, which prompts Blossom to smash her fist next to Eggman's face, cracking the mirror behind him.

Eggman further mocks the grieving teen, which prompts her to toss Eggman across the room. The Dr. staggers to his feet, further deriding the heroine over her belief that locking him away will magically reform him while walking over his chair as Blossom once again moves closer to him. Eggman then tells her to leave so he can escape and make further plains to 'top' the destruction oif Townsville. Pushed to her limit. Blossom snatches Eggman by his neck and lifts him off the ground.

Sonic tries to intervene but Blossom gently pushes him aside, knocking the blue Hedgehog flat on his back. As Blossom returns her attention to the scientist. Eggman manages to choke out one final insult, asking if will ever be the same ever again, and that she wouldn't kill another little boy, Blossom eyes flash red in fury as she draws her fist back, while Sonic watches in horror, and Eggman grins one more time, Blossom then kills Eggman by shoving her hand into his chest, ruthlessly killing the madman.

The plot cuts to an alternate universe where Bubbles is using her Sonic Scream on a fleeing Enejak while Blossom is grapples with Black Doom, the leader of the Black Arms army. Blossom disarms Black Doom's sword with her heat vision while Bubbles continues to chase after Enejak, though she's forced to stop when Enejak creates a spike shield construct to werd her off. As Bubbles continues to fly after Enejak, Cream furiously attacks Metal Sonic with Knuckles's help.

Blossom manages to defeat Black Doom, allowing Buttercup and Shadow to restrain him, before she can fly to the Ark to deal with the individual who was behind this attack, Mojo Jojo, The Werehog lands behind her, forcing her to contend the dark monster, but finds herself easily backhanded aside, leaving Buttercup and Shadow to handle the monster.

On the Ark, Wave blasts an armored Mojo Jojo with her sonic cannon. though her attacks are easily deflected by the ape's metal sult as he retaliates with missiles. Scourge is knocking Tails around when he sports Mojo's missiles heading towards their way and quickly moves aside to let Tails be struck, though the mobian by the G.U.N. spy, Rouge The Bat, who retaliates the missiles at Dark Oak, as the sinister alien gets Tails in a bear-hug, allowing her to gain the upper hand. Mojo and Rouge exchange banter before Tails is suddenly yanked away by Brick. Mojo tries to blast Rouge but she flys away and Wave is thrown across Ark by Nazo, landing next to Tails as Scourge approaches them. Tails contacts his best friend Sonic for assistance, but Sonic is heading to the No-Zone to ensure that Mojo didn't free Eggman. Despite Tails assurance, Sonic continues on his way after assuring Tails he'll be there soon.

An orderly leads Sonic to Eggman's cell but Sonic stops him from opening and reveals a trip wire and several explosives inside the cell. Sonic suddenly throws the zone cop out of the way and jumping into the air from the attack, Metal Sonic reveals himself to be under Mojo Jojo's orders and the one who freed Eggman. He attacks Sonic, but is easily outmatched and bested by the hero. As Sonic leaves the No-Zone, he attempts to contact Tails but can't reach him.

Back at Townsville, Knuckles tries to attack the Werehog but is easily held off, forcing Bubbles to intervene. working with Shadow, he knocks the Werehog out of the sky. Cream sees the monster falling as uses Chaos Control next to a weaken Flona, turning her back into a normal mobian just at the Werehog lands on her, Down at the streets below, Rob O' The Hedge and Jet the Hawk witness the fall, Rob saves the female fox from falling to her death. Though the Werehog begins to rise back up, further enraged, he is prevented from attacking the two by Blossom, who tackles into the beast into the sky while flying at full speed.

Back on the Ark, Wave pummels Nazo with punches while Rouge attempts to strike Brick with her skills. Tails valiantly attempts to defeat Scourge, but the villainous Hedgehog finally knocks him out with a powerful strike to his back. As Mojo watches his minions do his bidding, Sonic teleports onto the Ark behind him, Mojo then orders Scourge to deal with Sonic. Scourge threatens to break Sonic's back, but is instead bested by Sonic who moves on to Mojo.

Sonic weakens the ape's sult by throwing several Chaos Spares at his sult, andthen finishes him in a fight. Sonic then places a device on the ape's sult, deactivating it as Rouge and Tails lead his beaten cronies through a portal out of the Ark. Sonic then contacts Blossom and learns the other villains have been dealt with and the leader of the Powerpuff Girls is personally taking the Werehog into space. Just then an alarm sound through the Ark, Wave pulls up a screen and to Sonic horror, they see Eggman and Snively in the heart of Townsville with a nuclear device.

An iocredulous Sonic demands an explanation from Mojo Jojo, who reveals he to use Eggman to destroy Townsville, killing most of the Freedom Fighters so that he can swoop in as a hero to rebuild the city. Tails knocks him out as Sonic issues a code red and gives the Freedom Fighters and the Powerpuff Girls cordinates to Eggman.

In the heart of the city. Eggman arms the nuke while Snively watches before spotting Sonic teleport down close to him, Eggman orders Snively to leave, and when he protests, Eggman slapes him, forcing him to go. As Sonic hurriedly moves closer to Eggman, the madman takes the nuke off standby. The Freedom Fighters try to get closer to them.

Sonic tries to convince Eggman not to press the button, but Eggman raises the button for the nuke. The scene slows down as Sonic charges the madmam while the Freedom Fighters finally reach them. Strangely, Bubbles, Rob O' The Hedge, Shadow, Buttercup, Sonic and Eggman become engulfed in blue auras of energy before vanishing just as Sonic colides with Eggman.

The two arch foes land in a street of Townsville, though Sonic notes something is wrong, Eggman is furious that his trigger no longer works, and blaming Eggman, tries to attack him, though he is easily held off by Sonic's mobian strength, Eggman decides to kill Sonic and the two fought in the street, with Sonic emerging victorious. Sonic then subdues Eggman when several armed squads of soliders arrival, weapons aimed at both Sonic and Eggman. One of the soliders orders Sonic to put his hands up, and after seeing how vastly out numbered he is, he complies, but activates a supersonic disruptor he borrowed from Tails which causes all of the soliders to double in pain, Sonic then throws smoke grenades, allowing himself and Eggman to escape.

As Sonic looks down on this new Townsville, listening in on several radio chatters between the soliders, he murmurs to himself that he is in a nightmare.

Meanwhile, Bubbles, Buttercup, Shadow and Rob O' The Hedge are looking over a very different Central City, discussion what possibly happened to send them where they are. Deciding they have to their Townsville